MD Simulations of proton transport along a surface decorated with sulfonate groups

We analyse the proton distributions in slab simulations of models of characteristic aqueous pores in polymer electrolyte membranes utilized in low temperature hydrogen and direct methanol fuel cells. In particular we calculate density profiles across the interfacial region and density distributions parallel to the interface for aqueous systems near nonpolar surfaces covered with static or tethered sulfonate groups. Three different model descriptions have been used, two based on a previously employed fluxional empirical valence bond model, and one using rigid ion and water models. The goal is to identify common characteristics, which are to first approximation independent of the particular choice of the details of the interaction and geometrical model. We observe that lateral (diffusive) proton motion shows only small barriers for reasonable choices of the arrangement of SO3- groups and that there is a significant coupling between lateral motion and motion perpendicular to the pore surface. We provide structural evidence that previously proposed surface and bulk transport mechanisms in a polymer electrolyte are not distinct mechanisms. Instead we conclude that the simulations are consistent with a common structural diffusion mechanism, modified by the topology of the landscape around the sulfonate groups. (C) 2006 Elsevier B.V All rights reserved

First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids

We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to an overall of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.Comment: The reported data can be accessed in the NOMAD repository via the link http://dx.doi.org/10.17172/NOMAD/20150526220502 or on this website: http://aminoaciddb.rz-berlin.mpg.d